LOCUS       CP082446                2364 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1608038 plasmid pF18S023-2364, complete sequence.
ACCESSION   CP082446
VERSION     CP082446.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05964744
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Johannesburg
  ORGANISM  Salmonella enterica subsp. enterica serovar Johannesburg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2364)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2364)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 2364)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Assembly Name                     :: F18S023
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 531x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:30:53
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,873
            CDSs (total)                      :: 4,753
            Genes (coding)                    :: 4,630
            CDSs (with protein)               :: 4,630
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 62 of 123
            Pseudo Genes (incomplete)         :: 67 of 123
            Pseudo Genes (internal stop)      :: 23 of 123
            Pseudo Genes (multiple problems)  :: 26 of 123
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..2364
                     /organism="Salmonella enterica subsp. enterica serovar
                     Johannesburg"
                     /mol_type="genomic DNA"
                     /strain="FSIS1608038"
                     /serovar="Johannesburg"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:913076"
                     /plasmid="pF18S023-2364"
                     /geo_loc_name="USA:IA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            424..726
                     /locus_tag="BL362_001595"
     CDS             424..726
                     /locus_tag="BL362_001595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005161566.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /protein_id="UAE73787.1"
                     /translation="MSSMVYCRGCGKEIHETAKSCPHCGATNASSGSGEKSRIAAALLA
                     FFLGGFGVHKFYLGKIGQGFLYLIFCWTFIPAIIAFIEFIIYLCDSDEKFARKYG"
                     /name="NINE protein"
     gene            complement(869..1153)
                     /locus_tag="BL362_001600"
     CDS             complement(869..1153)
                     /locus_tag="BL362_001600"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE73788.1"
                     /translation="MDLEKALKEAETGYSLKLTSTDEAEMLAYISTVLELHAKGDLLHE
                     SAIDRVMTLCVLINTGNRQELSRTLRGFNNGGNWPSTTGNPSGGGRGNL"
                     /name="hypothetical protein"
     Typing          2..318
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="99.0"
                     /evalue="1.96e-57"
     Typing          1987..2364
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.306"
                     /coverage="81.0"
                     /evalue="8.88e-176"
ORIGIN
        1 gtatgcacga accccccgtt cagtccgacc gctgcgtctt ctccggtaac tatcgacttg
       61 agtccaagcc ggaaagacac gacaaagcgc cactggcagc agccactggt aactgattta
      121 gaggagttag tcttgaagtt atgcgcctgt taaggctaaa ctgaaagaac agatttggtt
      181 actgcgctcc tcataagcca gttaccacgg ttcaaagagt tgctgctctg agaaccttcg
      241 aaaaaccgcc ttgctgggcg gttttttcgt ttactgagca agagattacg acgctacaga
      301 aaggatctca agaagatcct tcaccataat ggaaatctat cccacccgag catataggat
      361 gcatatcgtt ataaaacatc ggatattatg catcccaact aaaaataagc tcgaggataa
      421 aaaatgagtt caatggttta ctgccgagga tgcggcaagg aaatacacga aacagcaaag
      481 tcatgcccac actgcggagc cacaaacgcc tcttcaggtt caggtgaaaa aagtagaatc
      541 gcagccgcgc tattagcatt cttccttggt ggatttggcg tacataaatt ttacttaggt
      601 aaaataggac agggattcct gtatctaatt ttttgctgga cattcatacc cgcgatcatc
      661 gcgtttattg agtttattat ttatctatgc gattccgatg aaaaattcgc aagaaaatat
      721 ggctaactca tagcaaaaaa gccctgcggg gctttttttg taccagtctg tgaggcagat
      781 ttaccataac atccgttgta cgcaacatgc agtaaagcct gctgagcgca ggctttacgt
      841 aaaaagcagg gtatgacgaa accaagtgtt agagattgcc ccgtccacca cctgatggat
      901 ttcccgtagt gctaggccag ttaccaccat tattaaaccc gcgaagcgtc cggcttaact
      961 cctgtcggtt tcctgtgtta ataagcacac ataatgtcat aaccctgtct atggcagact
     1021 catgtagtag gtcaccttta gcgtggagtt caagtacggt tgagatataa gccagcattt
     1081 cagcctcatc tgtactggtt aacttgaggc tatatccggt ttctgcttcc ttcagtgctt
     1141 tttctagatc cattttcaac cctctggttc attcaatact gcaacaaaat agcatatcaa
     1201 aacgagtcac aacgcaccgg catttaccat aacatctgtt gcccgcacct cctgagaacc
     1261 cctcagcgcg tttctgctgc ctctggcctg aaaaccgggg ttaagacccg ctaaaaacct
     1321 cttttaagcc actgttaatt tctgagcatg tgcatgtcta tgcacgcgaa cgcatgcccg
     1381 cgtttttagc agctaaaatc cgtcgaacgc cctgaaagcc atcatgaacc accctgataa
     1441 cggtgaacgg gtgcgcagtt tactgtgctg ccgtgaggtg ttggccaggc cgtcaggcat
     1501 ggaaggattt attgctaagg gggtcggatt taacgtggat gaatcagcac gcagtgatga
     1561 acgggattcg gaaggggcac ccttgcggcg cggcgatgta tacatcgcta acgtgccttg
     1621 gtcatttatt gcaagaaggg agaggtagca ttttgatagc aaaaaagtag caaaaggata
     1681 gcaaccgaaa gaccagaaga ctctggagat agcaaaaaag tagcaaaatg gtagcaaaaa
     1741 gatagcacac atgcgggagc taaccaggag tctttagcgg gccggcggta ctccaaaaac
     1801 acatattgtc ccgctgtttt gtgaataagc cagcatagct gtgggcacaa aacatttcct
     1861 gtccgctgct ttaacctttg taatccagga acgtcaggtg acgtcacttt gcggcgttag
     1921 ccctatcctg catcgtatta aaaaatgcag ctatggcgcg tacggtgcca aagataagcc
     1981 cggagatatt ccgcttcctc gctcactgac tcgctccgct cggtcgttcg gctgcggcga
     2041 gcggtaccgg cttactggcg gggcggaaat ttcctggcat cttccaggaa gaagcttaac
     2101 agggaagcaa gaaggccacg gcgaagccgt ttttccatag gctccgcccc cctgacaagc
     2161 atcacgaaat ctgacgctca aatcagtggt ggcgaaaccc gacaggactt aaagatacca
     2221 ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg
     2281 tgtcattccg ctgttatggc cgcgtttatc tcattccacg cctgacactc agttccgggt
     2341 aggcagttcg ctccaagctg gact
//
